Raised by Wolves on HBO Max is filled with chilling sci-fi mystery that deepens with each episode, leading many to speculate and resulting in a lot of unanswered questions for the upcoming season 2 to answer. One interesting question is why Father's eyes are blue like Mother's. At first glance, this question may not seem all that important, but a deeper look brings to light some interesting ideas.
While only the first two episodes of Raised by Wolves were directed by Ridley Scott, his DNA runs throughout the entire first season. In fact, despite the show being created by Aaron Guzikowski, some have speculated that Raised by Wolves exists on the same timeline as Scott's other science fiction work, such as Alien and Blade Runner. Whatever the case may be, Mother and Father are androids at the heart of the series, much like Michael Fassbender's David is the focal point of Scott's most recent contributions to the Alien universe, Prometheus and Alien: Covenant.
Mother, as it turns out, is a necromancer — a powerful android capable of using her eyes, along with a piercing scream, to kill. Father, on the other hand, is a simple service model android, designed to help with everyday tasks and little else. Interestingly, Mother's non-necromancer eyes are brown, but when she takes them out and replaces them with her blue necromancer eyes, she can kill anyone who looks at her. Father's eyes are also strikingly blue. Is there a reason for this? It could be a coincidence, but it could also mean that Father is carrying an extra set of necromancer eyes in case Mother were to lose her original ones.
Father's blue eyes are striking from the very first episode of Raised by Wolves. They give him an android look despite his human appearance. Father was sent to accompany Mother on their mission to raise human children on Kepler-22B. Their creator, Campion Sturges, puts a lot of effort into re-programming Mother for this task. He captures her as a necromancer and then labors to train her to always protect and never hurt her children. When he has completed this task, he sends Mother on her way, introducing her to Father offhandedly, as if Father was added to the mission as an afterthought. His sole purpose seems to be to support Mother and to help her, no matter what. It could be that this mission extends even further, with his body serving as extra parts just in case Mother breaks any.
If this is the case, it's possible that Father's eyes are meant to be an extra set for Mother. By the end of Raised by Wolves season 1, Mother's eyes remain in the possession of Marcus, although the Mithraic soldiers shove one of them into his mouth after beating him at the end of episode 9, "Umbilical." This could mean that Mother's necromancer eyes are now damaged and useless, making her an android no more powerful than Father. Unless, of course, Mother is able to borrow Father's eyes to revert to her necromancer form. However this pans out in Raised by Wolves season 2, it's likely Mother will need her deadly abilities to take on the giant snake creature and the newly arrived atheists if she is going to continue to protect the children as Campion programmed her to do.